Research in the Barker Lab

We study the origins of biological diversity, particularly how abrupt genomic events such as polyploidy (genome duplication), chromosomal change, and hybridization have contributed to the evolution and diversity of life. Biologists have long been fascinated by these processes because they create unique opportunities for the evolution of novelty with the potential for relatively rapid diversification. While assessing the roles of these genomic changes in evolution has historically been a difficult task, advances in genomics and computational biology have created new opportunities for addressing these longstanding questions. Our research program integrates new computational and evolutionary genomic tools with traditional approaches such as molecular evolution, phylogenetics, mathematical modeling, and experimental work to better understand the origins of biological diversity. We use a combination of publicly available genomic data and new data generated by ourselves and collaborators from a diverse set of study systems. Our ultimate goal is to connect patterns of genome evolution across time scales by leveraging systems where we can study microevolutionary processes to inform our understanding of macroevolutionary patterns.

Some of the questions we are currently researching

How does polyploidy influence rates of adaptation and speciation? Do changes in the efficacy of selection in polyploids lead to higher rates of adaptation or impede evolution relative to diploids? How may the population genetics of polyploid species influence their macroevolutionary outcomes?

Why do polyploid species diploidize if they were successful as polyploids? Does natural selection or drift drive diploidization?

Are there universal rules that govern genome evolution following genome duplication? What are the relative roles of natural selection and drift driving the retention and loss of genes following polyploidy? Does dosage-balance constrain the evolution of large fractions of paleopolyploid genomes?

How do multiple origins of polyploid species contribute to polyploid success? Does a single genome organization emerge from multiple origins? If so, does selection or drift drive the evolution of genome organization from multiple origins? Are polyploids of different origins interfertile?

How does hybridization influence the evolutionary success of polyploids? Do allopolyploids or autopolyploids have an evolutionary advantage? Does hybridization (and polyploidy) itself create evolutionary novelty or does simply cutting off gene flow from the broader species range allow rare genotypes to persist and proliferate?

Why do rates of chromosome gain and loss vary dramatically across the phylogeny? How do these rates impact diploidization following polyploidy? What evolutionary forces drive the gain and loss of chromosomes, and ultimately the evolution of chromosome number?

Systems we are currently studying in our lab:

Selaginella: a local group of lycophytes with some of the smallest plant genomes (smaller than Arabidopsis!). These plants dessicate during dry periods and resurrect when it is wet again. They can be resurrected from collections, including 100 year old herbarium sheets! We are working on a number of local hybrids and polyploid species that occur on the Madrean Sky Islands. The Sky Islands create natural barriers to gene flow among populations and provide interesting evolutionary experiments for us to explore. Focal species currently include S. arizonica, S. eremophila and their diploid and polyploid hybrids as well as the allotetraploid S. rupincola. We use these species to study the population genomics of hybridization and polyploidy in plants.

Brassica: We are currently studying how polyploidy contributed to the diversity of the crop Brassicas (e.g., broccolii, cauliflower, kale, cabbage, etc.). These crops are a model agricultural system for understanding how changes in natural selection and genetic variation following polyploidy may drive diversity.

The Hawaiian Silversword Alliance: An outstanding adaptive radiation of more than 35 species of composites on the Hawaiian islands. Following allopolyploid speciation, these species radiated into nearly every habit (vines, trees, shrubs, etc) and life history observed in plants. We are studying how hybridization and genome duplication contributed to this amazing radiation. The Hawaiian Silversword Alliance is an amazing model system for exploring hypotheses of how polyploidy may drive the diversification of plants.

Plants, insects, vertebrates, and everything in between: To better understand the history of polyploidy in the evolution of life on earth we use our bioinformatic tools to document and analyze paleopolyploidy across the tree of life. Numerous public (e.g, 1KP) projects are generating phylogenetically broad genomic data that we analyze. If you have a favorite group of organisms with new genomic data, chances are we would like to analyze them!

>

Bioinformatic Methods Development

We also actively develop and maintain a suite of evolutionary bioinformatic tools to facilitate our research. Our tools are currently hosted at our public facing server, EvoPipes.net. Currently, we are developing new and efficient bioinformatic software for identifying and analyzing ancient whole genome duplications and hybridization. If you are interested in software or bioinformatic algorithms, we would be happy to have you join us!

Interested in Joining the Lab?

We are always looking for new people to join the lab at all levels. We are currently accepting graduate students for the upcoming Fall 2016 round of admissions. We are also looking for new postdocs that may be interested in applying for NSF Biology Postdocs, NIH Postdocs, UA EEB's Simpson Postdoctoral Fellowship, and UA's PERT Postdoc Program. PERT applications are currently being accepted and I strongly encourage all candidates, even those with botanical backgrounds, to look at the program. Although PERT has a focus on insects, please contact Dr. Barker to discuss our recent work on insect evolution and plant-insect interactions.